extract extra info (logs) from history

extract extra info (logs) from history

Hi,

I would like to use the info (log) HISAT is showing, for another tool.
e.g.:
26781724 reads; of these:
26781724 (100.00%) were unpaired; of these:
2445411 (9.13%) aligned 0 times
20399099 (76.17%) aligned exactly 1 time
3937214 (14.70%) aligned >1 times
90.87% overall alignment rate
[bam_sort_core] merging from 21 f

Is it possible to access these logs?

Cheers Jochen
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> That's also an interesting tool. Which gives almost the same result as in
> the log file of at HISAT output. I'm not sure why the number of mapped reads
> are not 100% identical...
>
> but anyway can someone tell me, or maybe Devon did already, where is the log
> info of HISAT saved?
>
> Cheers Jochen
>
>
>
> On 02.05.2018 12:37, Langhorst, Brad wrote:
>>
>> Flagstat might be a good choice here…
>>
>> Brad
>>
>>> On May 2, 2018, at 1:48 AM, Jochen Bick <[hidden email]> wrote:
>>>
>>> Hi Devon,
>>>
>>> do you mean Alignment Summary? How can I access that information and use
>>> it for an other tool.
>>>
>>> Cheers Jochen
>>>
>>>
>>> On 26.04.2018 14:14, Devon Ryan wrote:
>>>>
>>>> There are two alignment summary options in the wrapper that will cause
>>>> most/all of that to be written to a history item. They're under
>>>> "Summary Options".
>>>>
>>>> Devon
>>>> --
>>>> Devon Ryan, Ph.D.
>>>> Email: [hidden email]>>>> Data Manager/Bioinformatician
>>>> Max Planck Institute of Immunobiology and Epigenetics
>>>> Stübeweg 51
>>>> 79108 Freiburg
>>>> Germany
>>>>
>>>>
>>>> On Thu, Apr 26, 2018 at 2:11 PM, Jochen Bick <[hidden email]>
>>>> wrote:
>>>>>
>>>>> Hi,
>>>>>
>>>>> I would like to use the info (log) HISAT is showing, for another tool.
>>>>> e.g.:
>>>>> 26781724 reads; of these:
>>>>> 26781724 (100.00%) were unpaired; of these:
>>>>> 2445411 (9.13%) aligned 0 times
>>>>> 20399099 (76.17%) aligned exactly 1 time
>>>>> 3937214 (14.70%) aligned >1 times
>>>>> 90.87% overall alignment rate
>>>>> [bam_sort_core] merging from 21 f
>>>>>
>>>>>
>>>>> Is it possible to access these logs?
>>>>>
>>>>> Cheers Jochen
>>>>> ___________________________________________________________
>>>>> Please keep all replies on the list by using "reply all"
>>>>> in your mail client. To manage your subscriptions to this
>>>>> and other Galaxy lists, please use the interface at:
>>>>> https://lists.galaxyproject.org/>>>>>
>>>>> To search Galaxy mailing lists use the unified search at:
>>>>> http://galaxyproject.org/search/>>>
>>> ___________________________________________________________
>>> Please keep all replies on the list by using "reply all"
>>> in your mail client. To manage your subscriptions to this
>>> and other Galaxy lists, please use the interface at:
>>> https://lists.galaxyproject.org/>>>
>>> To search Galaxy mailing lists use the unified search at:
>>> http://galaxyproject.org/search/>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client. To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
> https://lists.galaxyproject.org/>
> To search Galaxy mailing lists use the unified search at:
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Re: extract extra info (logs) from history

I think now I got it ;-). We are running 17.05 I might not have the
"Summary Options" ? I cannot find them...

But maybe I can use the flagstat tool for now.

Cheers Jochen

On 02.05.2018 16:34, Devon Ryan wrote:

> By default the logs are just to stdout. You need to use one of the
> options (under "Summary Options" on the version on our instance) if
> you want things saved as a history item.
>
> Devon
> --
> Devon Ryan, Ph.D.
> Email: [hidden email]> Data Manager/Bioinformatician
> Max Planck Institute of Immunobiology and Epigenetics
> Stübeweg 51
> 79108 Freiburg
> Germany
>
>
> On Wed, May 2, 2018 at 4:32 PM, Jochen Bick <[hidden email]> wrote:
>> That's also an interesting tool. Which gives almost the same result as in
>> the log file of at HISAT output. I'm not sure why the number of mapped reads
>> are not 100% identical...
>>
>> but anyway can someone tell me, or maybe Devon did already, where is the log
>> info of HISAT saved?
>>
>> Cheers Jochen
>>
>>
>>
>> On 02.05.2018 12:37, Langhorst, Brad wrote:
>>> Flagstat might be a good choice here…
>>>
>>> Brad
>>>
>>>> On May 2, 2018, at 1:48 AM, Jochen Bick <[hidden email]> wrote:
>>>>
>>>> Hi Devon,
>>>>
>>>> do you mean Alignment Summary? How can I access that information and use
>>>> it for an other tool.
>>>>
>>>> Cheers Jochen
>>>>
>>>>
>>>> On 26.04.2018 14:14, Devon Ryan wrote:
>>>>> There are two alignment summary options in the wrapper that will cause
>>>>> most/all of that to be written to a history item. They're under
>>>>> "Summary Options".
>>>>>
>>>>> Devon
>>>>> --
>>>>> Devon Ryan, Ph.D.
>>>>> Email: [hidden email]>>>>> Data Manager/Bioinformatician
>>>>> Max Planck Institute of Immunobiology and Epigenetics
>>>>> Stübeweg 51
>>>>> 79108 Freiburg
>>>>> Germany
>>>>>
>>>>>
>>>>> On Thu, Apr 26, 2018 at 2:11 PM, Jochen Bick <[hidden email]>
>>>>> wrote:
>>>>>> Hi,
>>>>>>
>>>>>> I would like to use the info (log) HISAT is showing, for another tool.
>>>>>> e.g.:
>>>>>> 26781724 reads; of these:
>>>>>> 26781724 (100.00%) were unpaired; of these:
>>>>>> 2445411 (9.13%) aligned 0 times
>>>>>> 20399099 (76.17%) aligned exactly 1 time
>>>>>> 3937214 (14.70%) aligned >1 times
>>>>>> 90.87% overall alignment rate
>>>>>> [bam_sort_core] merging from 21 f
>>>>>>
>>>>>>
>>>>>> Is it possible to access these logs?
>>>>>>
>>>>>> Cheers Jochen
>>>>>> ___________________________________________________________
>>>>>> Please keep all replies on the list by using "reply all"
>>>>>> in your mail client. To manage your subscriptions to this
>>>>>> and other Galaxy lists, please use the interface at:
>>>>>> https://lists.galaxyproject.org/>>>>>>
>>>>>> To search Galaxy mailing lists use the unified search at:
>>>>>> http://galaxyproject.org/search/>>>> ___________________________________________________________
>>>> Please keep all replies on the list by using "reply all"
>>>> in your mail client. To manage your subscriptions to this
>>>> and other Galaxy lists, please use the interface at:
>>>> https://lists.galaxyproject.org/>>>>
>>>> To search Galaxy mailing lists use the unified search at:
>>>> http://galaxyproject.org/search/>>
>> ___________________________________________________________
>> Please keep all replies on the list by using "reply all"
>> in your mail client. To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>> https://lists.galaxyproject.org/>>
>> To search Galaxy mailing lists use the unified search at:
>> http://galaxyproject.org/search/

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Re: extract extra info (logs) from history

> On 2. May 2018, at 16:40, Jochen Bick <[hidden email]> wrote:
>
> Thanks Devon,
>
> I think now I got it ;-). We are running 17.05 I might not have the "Summary Options" ? I cannot find them...
>
> But maybe I can use the flagstat tool for now.
>
> Cheers Jochen
>
>
>> On 02.05.2018 16:34, Devon Ryan wrote:
>> By default the logs are just to stdout. You need to use one of the
>> options (under "Summary Options" on the version on our instance) if
>> you want things saved as a history item.
>>
>> Devon
>> --
>> Devon Ryan, Ph.D.
>> Email: [hidden email]>> Data Manager/Bioinformatician
>> Max Planck Institute of Immunobiology and Epigenetics
>> Stübeweg 51
>> 79108 Freiburg
>> Germany
>>
>>
>>> On Wed, May 2, 2018 at 4:32 PM, Jochen Bick <[hidden email]> wrote:
>>> That's also an interesting tool. Which gives almost the same result as in
>>> the log file of at HISAT output. I'm not sure why the number of mapped reads
>>> are not 100% identical...
>>>
>>> but anyway can someone tell me, or maybe Devon did already, where is the log
>>> info of HISAT saved?
>>>
>>> Cheers Jochen
>>>
>>>
>>>
>>>> On 02.05.2018 12:37, Langhorst, Brad wrote:
>>>> Flagstat might be a good choice here…
>>>>
>>>> Brad
>>>>
>>>>> On May 2, 2018, at 1:48 AM, Jochen Bick <[hidden email]> wrote:
>>>>>
>>>>> Hi Devon,
>>>>>
>>>>> do you mean Alignment Summary? How can I access that information and use
>>>>> it for an other tool.
>>>>>
>>>>> Cheers Jochen
>>>>>
>>>>>
>>>>>> On 26.04.2018 14:14, Devon Ryan wrote:
>>>>>> There are two alignment summary options in the wrapper that will cause
>>>>>> most/all of that to be written to a history item. They're under
>>>>>> "Summary Options".
>>>>>>
>>>>>> Devon
>>>>>> --
>>>>>> Devon Ryan, Ph.D.
>>>>>> Email: [hidden email]>>>>>> Data Manager/Bioinformatician
>>>>>> Max Planck Institute of Immunobiology and Epigenetics
>>>>>> Stübeweg 51
>>>>>> 79108 Freiburg
>>>>>> Germany
>>>>>>
>>>>>>
>>>>>> On Thu, Apr 26, 2018 at 2:11 PM, Jochen Bick <[hidden email]>
>>>>>> wrote:
>>>>>>> Hi,
>>>>>>>
>>>>>>> I would like to use the info (log) HISAT is showing, for another tool.
>>>>>>> e.g.:
>>>>>>> 26781724 reads; of these:
>>>>>>> 26781724 (100.00%) were unpaired; of these:
>>>>>>> 2445411 (9.13%) aligned 0 times
>>>>>>> 20399099 (76.17%) aligned exactly 1 time
>>>>>>> 3937214 (14.70%) aligned >1 times
>>>>>>> 90.87% overall alignment rate
>>>>>>> [bam_sort_core] merging from 21 f
>>>>>>>
>>>>>>>
>>>>>>> Is it possible to access these logs?
>>>>>>>
>>>>>>> Cheers Jochen
>>>>>>> ___________________________________________________________
>>>>>>> Please keep all replies on the list by using "reply all"
>>>>>>> in your mail client. To manage your subscriptions to this
>>>>>>> and other Galaxy lists, please use the interface at:
>>>>>>> https://lists.galaxyproject.org/>>>>>>>
>>>>>>> To search Galaxy mailing lists use the unified search at:
>>>>>>> http://galaxyproject.org/search/>>>>> ___________________________________________________________
>>>>> Please keep all replies on the list by using "reply all"
>>>>> in your mail client. To manage your subscriptions to this
>>>>> and other Galaxy lists, please use the interface at:
>>>>> https://lists.galaxyproject.org/>>>>>
>>>>> To search Galaxy mailing lists use the unified search at:
>>>>> http://galaxyproject.org/search/>>>
>>> ___________________________________________________________
>>> Please keep all replies on the list by using "reply all"
>>> in your mail client. To manage your subscriptions to this
>>> and other Galaxy lists, please use the interface at:
>>> https://lists.galaxyproject.org/>>>
>>> To search Galaxy mailing lists use the unified search at:
>>> http://galaxyproject.org/search/>

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